fitSingle: Driver Routine - Uncoupled Spatial Model

In predsci/DICE: DICE: Dynamics of Interacting Community Epidemics

Description

A spatially uncoupled MCMC fit of the model data. The code first fits the model data directly and then fits each of the sub-regions sequentially - minimizing the likelihood of each one. The final indirect model fit is obtained as a weighted sum of these individual fits with the weights given by the relative population of each region. The data can be either cdc or gft data, and the model/fit data should have different spatial scales. For example in the case of cdc/gft data: the model can be national and the fit are the ten HHS regions. Or the model can be an HHS region and the fit are the states in that region.

Usage

fitSingle(mydata = NULL, all_years_epi = NULL, opt.list = NULL,
  run.list = NULL, ireal = 1, iseed = NULL)

Arguments

mydata	A complex list with all available data for a given season model/fit spatial levels and data type
all_years_epi	A complex list with all available data for all seasons model/fit spatial levels and data type
opt.list	A Logical list with TRUE or FALSE values for all the parameters supported by DICE. These values are set based on the user chosen model for the basic reproduction value.
run.list	A list with parameters needed for the MCMC procedure
ireal	Integer - the MCMC chain number. Default is 1. #' @param iseed An integer used to set the random-number-generator seed. When not specified, the seed is generated randomly. Setting the seed to a known integer allows an MCMC chain to be reproducible.

Value

A list with the following arguments:

model_rtn

The best result of the MCMC procedure for the model data

model_profile

Randomly selected results from the MCMC procedure of directly fitting the model data

tab.model

The MCMC history of the direct fit to the model data

fit_rtn

The best result for indirectly fitting the model data using the fit regions

fit_profile

Randomly selected results from the MCMC procedure of indirectly fitting the model data using the fit regions

tab.fit

The MCMC history of indirectly fitting the model data using the fit regions

Examples

fitSingle{mydata = mydata, opt.list = opt.list, run.list = run.list, ireal = ireal, iseed = iseed}

predsci/DICE documentation built on Aug. 9, 2019, 9:41 a.m.